Hello there, I am trying to generate some DE tables using RNA-Seq data in Limma but I am getting this error message:
Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8”
In addition, why does my annotation file have 37,302 lines, while my feature count file has only 27,180 lines?
This is my history: Galaxy
Thanks for your time.
Hi @XIANG_CHI
Overall solution → try following the instructions in this tutorial to set up the count/factor files → Hands-on: 2: RNA-seq counts to genes / Transcriptomics
To use the Contrasts of Interest function, you need a Factor file. Then to use a Factor file, you need a Count matrix or individual samples with proper labeling (not the auto-generated “HISAT2 on …” type of default labels), which loops back to the example in that tutorial. Technically, you can also just review the examples down in the Help section of the tool form if you already know how to do text manipulations. Once all the data keys match up together across inputs, this will work fine.
Hope this helps and thanks for sharing the history! Sped things up! 
Full stderr log
Warning message:
In Sys.setlocale(“LC_MESSAGES”, “en_US.UTF-8”) :
OS reports request to set locale to “en_US.UTF-8” cannot be honored
Error in [<-.data.frame(*tmp*, files, factorname, value = “N15”) :
column name “” cannot match any column
Calls: [<- → [<-.data.frame
